PNNL-13501 - Pacific Northwest National Laboratory

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Contents Director’s Statement................................................................................................................................................................vii Introduction ............................................................................................................................................................................viii LDRD Program Management .................................................................................................................................................ix Peer Review and Self-Assessment............................................................................................................................................xi Analytical and Physical Chemistry Advanced Methodology for the Analysis of Organic Components .............................................................................................1 Complex Mixture Modeling for Occupation Exposure Assessment............................................................................................4 Development of New Laser-Mass Spectrometric Method for the Detection of Low Volatility Compounds in Particulate Matter.........................................................................................................................................................................6 Dynamics Study of Surface-Induced Dissociation Process .........................................................................................................8 High Efficiency Chromatographic Separations for Support of Biological Warfare Threats for Law Enforcement Agencies...............................................................................................................................................................10 Integrated Microfabricated Devices for Rapid and Automated Identification of Biological Agents.........................................13 Matrix Assisted Laser Desorption/Ionization Using Resonant Laser Ablation .........................................................................15 Molecular Beam Synthesis and Characterization of Nanoporous Catalytic Materials ..............................................................17 Native Aerosols: Their Composition, Distribution, Reactivity, and Coupling to Tropospheric Chemistry..............................20 Surface-Induced Dissociation of Polyatomic Cations................................................................................................................23 Ultrasensitive Studies of Reactive Aerosols ..............................................................................................................................25 Biosciences and Biotechnology Analysis of Receptor-Modulated Ion Channel Signaling by Confocal Optical/Patch-Clamp Microscopy ...............................31 Automated DNA Fingerprinting Microarrays for Environmental Epidemiology of Pathogenic Microorganisms....................35 Biologically-Based Dose-Response Models for Low Dose Exposures to Chemicals and Radionuclide Mixtures ...................38 Biomolecular Interaction Assay System....................................................................................................................................41 Characterization of Global Gene Regulation by Tumor Necrosis Factor Alpha in Genetically Defined Mice .........................45 Characterization of Nodes in Cell-Signaling Pathways Using High-Throughput Array Technologies.....................................48 Coupled NMR and Confocal Microscopy for In Situ, Real Time Cellular Measurement Capabilities .....................................53 Development and Applications of a Multifunctional Optical Microscope for Mapping Cellular Signaling Pathways .............57 Development of a New High Throughput Technology and Data Analysis Capabilities for Proteomics ...................................60 Development of the Recombinant Protein Expression <strong>Laboratory</strong>............................................................................................64 Discovery, Isolation, and Characterization of Strong Plant Promoters......................................................................................66 Endocrine Disruption in the Built Environment ........................................................................................................................69 Fungal Conversion of Agricultural Waste Glucose/Cellulose Materials to Malonic Acid ........................................................71 Fungal Conversion of Waste Glucose/Cellulose Materials: Organic Solvents/Organic Acids.................................................73 Fungal Molecular Biology: Promoter Isolation and Characterization ......................................................................................76 Improving H2 Production by Rational Enzyme Redesign..........................................................................................................79 Isoprostane-Mediated Tumor Promotion...................................................................................................................................81 Microbial Siderophore Role in Metal Uptake by Oats and Crested Wheatgrass .......................................................................84 NMR-Based Structural Genomics .............................................................................................................................................87 Plant Root Exudates and Microbial Gene Expression in the Rhizosphere.................................................................................91 Rapid NMR Determination of Large Protein Structures............................................................................................................95 Role of Unculturable Bacteria in the Wheat Rhizosphere .........................................................................................................97 Contents iii
Computational Science and Engineering Code Development for NWGrid/NWPhys ..............................................................................................................................103 Collaborative Problem-Solving Environments ........................................................................................................................106 Combustion Simulation and Modeling ....................................................................................................................................109 Conservation Laws in Support of Reactive Transport .............................................................................................................112 Development of Models of Cell-Signaling Pathways and Networks.......................................................................................117 Distributed, Real-Time Decision Support Environments ........................................................................................................122 Framework for Integrating Multiple Platform Computational Models....................................................................................124 Free-Surface Hydrodynamics and Fish Behavior Simulation..................................................................................................127 HostBuilder: A Tool for the Combinatorial Generation of Host Molecules...........................................................................130 Invariant Discretization Methods for n-Dimensional Nonlinear Computational Reactive Transport Models.........................132 Lattice Boltzmann Methods.....................................................................................................................................................136 Mixed Hamiltonian Methods for Geochemical Electronic Structure Studies ..........................................................................138 Modeling Ras:Ras-Effector Complexes: Key Components of Stress-Signal Transmission ...................................................141 Simulation and Modeling of Electrochemistry and Performance Assessment of Solid Oxide Fuel Stacks.............................144 Computer Science and Information Technology Advanced Anomaly Detection.................................................................................................................................................149 Bioinformatics for High-Throughput Proteomic and Genomic Analysis ................................................................................155 Collaborative Environments for Large Information Spaces ....................................................................................................156 Critical Infrastructure and Protection Simulator (CIPS)..........................................................................................................158 Interactive Network Traffic Modeling.....................................................................................................................................160 Mathematical Learning of Patterns and Exceptions from Text................................................................................................162 Non-Verbal Communication in Virtual Collaborative Environments .....................................................................................164 The DNA Approach to Organic Data Memory........................................................................................................................167 Visualization and Active Guidance of Scientific Computations..............................................................................................169 Design and Manufacturing Engineering Development of Modeling Tools for Joining of Multicomponent Lightweight Structures .....................................................175 Integrated Modeling and Simulation for Fabrication of Lightweight Structures.....................................................................179 Joining of Dissimilar Materials for Lightweight Automotive..................................................................................................186 Modeling of High-Velocity Forming for Lightweight Materials Applications........................................................................189 Virtual Modeling and Simulation Environment.......................................................................................................................192 Earth System Science An Engineering Design Tool for Redox Barriers ....................................................................................................................197 Biogeochemical Processes and Microbial Characteristics Across Groundwater Surfaces ......................................................200 Development and Validation of Mesocosms for Experimentally Investigating Carbon Dioxide Sequestration in Wetlands ..............................................................................................................................................................................203 Development of a Tool for Investigating Multiphase and Multiscale Atmospheric Chemical and Physical Processes ..........207 Development of an Aquatic Bio-Optical Monitoring Buoy.....................................................................................................211 Electrochemical Enhancement of Permeable Treatment Barriers............................................................................................213 Enhancing Emissions Pre-Processing Capabilities for Atmospheric Chemistry .....................................................................216 Environmental Fate and Effects of Deep Ocean Carbon Sequestration...................................................................................218 Extension of Site Soil/Plant Physical Properties to Landscape and Regional Scales Using Remote Sensing.........................221 Impacts of CO2 Injection on Deep Geologic Formations ........................................................................................................224 In Situ Destruction of Contaminants Using Ozone..................................................................................................................228 Interrelationships Between Processes Controlling Loading Level, Release Rate, and Biological Activity of Contaminated Porous Media ...............................................................................................................................................230 Modeling the Sequestration of CO2 in Deep Geological Formations ......................................................................................233 Oxidation of Volatile Organics Leading to Tropospheric Aerosol Formation.........................................................................235 Prototype Regional Climate Collaboration Center ..................................................................................................................238 The Nature, Occurrence, and Origin of Atmospheric Aerosols and Their Role in Gas-Particle Chemistry............................242 Thermodynamics and Kinetics of Cation Exchange at Defects in Micas ................................................................................245 iv FY 2000 <strong>Laboratory</strong> Directed Research and Development Annual Report
Page 1 and 2: Laboratory Directed Research and De
Page 3: Laboratory Directed Research and De
Page 7 and 8: Policy and Management Sciences Asse
Page 9 and 10: Introduction Department of Energy O
Page 11 and 12: 5. After reviews by the Technical a
Page 13 and 14: • The Technical Council peer revi
Page 15 and 16: methods applicable to combustion, s
Page 17 and 18: Summary Each national laboratory mu
Page 19 and 20: Study Control Number: PN0004/1411 A
Page 21 and 22: Table 1. Positive and negative ions
Page 23 and 24: m/z Arbitrary Units Figure 1. Mass
Page 25 and 26: introduce low-volatility compounds
Page 27 and 28: arrangement, but the charge is reta
Page 29 and 30: two liquid chromatographic gradient
Page 31 and 32: Integrated Microfabricated Devices
Page 33 and 34: Matrix Assisted Laser Desorption/Io
Page 35 and 36: Molecular Beam Synthesis and Charac
Page 37 and 38: temperature distribution of the des
Page 39 and 40: expected to result in significant a
Page 41 and 42: Study Control Number: PN99069/1397
Page 43 and 44: Study Control Number: PN99073/1401
Page 45 and 46: Seuss DT and KA Prather. 1999. “M
Page 47 and 48: Analysis of Receptor-Modulated Ion
Page 49 and 50: laboratory (Lu and Xie 1997; Lu et
Page 51 and 52: Automated DNA Fingerprinting Microa
Page 53 and 54: Comparison of 4 Xanthomonas Isolate
Page 55 and 56:
Approach Hematopoietic (bone marrow
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Study Control Number: PN99005/1333
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Anti-Human lgG Human lgG Protein G
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Characterization of Global Gene Reg
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PCR products for immobilization on
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identify novel proteins of importan
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Immunoprecipitaton of tyrosinephosp
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Coupled NMR and Confocal Microscopy
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In the optical microscopy image, th
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Development and Applications of a M
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Figure 3. Hepa-1 cells undergoing a
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cellular processing (such as post-t
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8. Initial demonstration of an off-
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expression systems for several year
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accumulation of protein products, i
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Fungal Conversion of Agricultural W
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Fungal Conversion of Waste Glucose/
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Summary and Conclusions We demonstr
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are shown in Figure 1(a) and 1(b),
Page 95 and 96:
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Anchorage-Independent Growth (% con
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selection of seedlings demonstratin
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NMR-Based Structural Genomics Micha
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Solution-State Structure and Fold-C
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Plant Root Exudates and Microbial G
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98 99 100 6 7 10 3 1 12 11 15 16 17
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Summary and Conclusions • The gre
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Jones-Oliveira JB, JS Oliveira, HE
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• securely moves files to a targe
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Plenary invited lecture, “The Ele
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Figure 1. X3DGEN tetrahedral mesh o
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Figure 5a. OSO volume rendering of
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Development of Models of Cell-Signa
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SOS p 23 EGFR Professor Rodland at
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Oliveira JS, JB Jones-Oliveira, and
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Figure 2. Associating a dataset mar
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to 1) incorporate three-dimensional
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shown in Figure 1. Simulated result
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HostBuilder: A Tool for the Combina
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Invariant Discretization Methods fo
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Graphics, Inc., workstation. The co
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Mixed Hamiltonian Methods for Geoch
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guyanaite, and grimaldiite (see Fig
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in the Environmental Molecular Scie
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Simulation and Modeling of Electroc
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Summary and Conclusions We implemen
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Since the implementation of the gen
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asis of previous performance, perce
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Bioinformatics for High-Throughput
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Summary and Conclusions In previous
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User Cat - Supervisor (client) Anal
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The second goal was to research way
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Figure 1. A visualization technique
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and interactions. The flexibility o
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Figure 4. A filtered version of Fig
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Development of Modeling Tools for J
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Figure 2. Schematic of experimental
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Integrated Modeling and Simulation
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(a) (b) (c) (d) Figure 1. Results o
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Thurman DA. August 2000. Collaborat
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MARC Input initial m esh and result
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(Johnson 1999; Colligan 1999; Gould
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Modeling of High-Velocity Forming f
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Global divergence error 1 10 -14 0
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that users were unlikely to appreci
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Earth System Science
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the lateral extent of the plume so
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Biogeochemical Processes and Microb
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Analyses of populations of viable a
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The first task was to establish fiv
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purged for 2 minutes. The gas sampl
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developing code architecture to min
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Berkowitz, CM. June 2000. “Atmosp
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environmental monitoring, 2) portab
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corresponded to a current density o
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Enhancing Emissions Pre-Processing
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Environmental Fate and Effects of D
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nitrogen and unpredictable eutrophi
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Figure 1. Ordinary kriging of 2 m d
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precipitation of calcite occurred i
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Interrelationships Between Processe
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phenanthrene resistant fraction con
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injection of an immiscible gas phas
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still some key kinetic issues that
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Application of a Crop Model The res
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The Nature, Occurrence, and Origin
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Particle number concentration, 1/cm
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geometry optimized AlOOH and FeOOH
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allowable parameters using thermody
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TCE + 3H + + 3Fe 2+ Fe)=> acetylene
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Use of Shear-Thinning Fluids for In
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concentration of 0.5% AMX was the m
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Roberts AL, LA Totten, WA Arnold, D
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tetra-scale computing, envisioned a
Page 272 and 273:
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Energy Technology and Management
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Figure 2. Setup for the second expe
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phase. The algorithms will be teste
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[Pb-212]/[Pb-212] final 100 10 1 0.
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Plasma Particle Dielectric Fiber El
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(species, sub-species, and sex), sp
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Figure 3. Relative risk of bone and
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Development of a Preliminary Physio
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Development of a Virtual Respirator
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Figure 3. Use of the chest cavity a
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Examination of the Use of Diazolumi
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Indoor Air Pathways to Nuclear, Che
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Source Building Release Observed re
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To illustrate the potential impact
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Non-Invasive Biological Monitoring
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Materials Science and Technology
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Figure 1. (a) - (c) Successive magn
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Component Fabrication and Assembly
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Development of a Low-Cost Photoelec
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elaxations, indicating the adequacy
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Promising chemical durability, as m
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Study Control Number : PN98028/1274
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High Power Density Solid Oxide Fuel
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Hybrid Plasma Process for Vacuum De
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Matson DW, PM Martin, WD Bennett, J
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We showed the proof-of-principle ap
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Bandgap Energy (eV) 2.9 2.85 2.8 2.
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Ultrathin Electrolyte Test Results
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Detailed Investigations on Hydrogen
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identified low energy step structur
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Development of Novel Photo-Catalyst
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-2 -1 Energy (eV) 0 1 2 Cu2O SrTiO3
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Here, we perform adsorption and des
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exceed those in the all-metal devic
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Intensity (a.u.) 0 100 200 300 400
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integrated voltage (V) 0.10 0.08 0.
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The first step was to implement thi
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Spontaneous Formation of Cu2O Nano-
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Actinide Chemistry at the Aqueous-M
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Figure 5. Close-up atomic force mic
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to 300°C and 400°C. Unfortunately
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Summary and Conclusions Transmutati
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Advanced Calibration/Registration T
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Figure 1a. Violet filter Figure 1b.
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Autonomous Ultrasonic Probe for Pro
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containing nitrous oxide, an optica
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Chemical Detection Using Cavity Enh
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Figure 3 is a color rendered simula
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appropriate study has been performe
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Exploitation of Conventional Chemic
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Figures 3 and 4 illustrate the impa
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enefits of using a modified spread-
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Single Channel Signal 0.0025 0.0020
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Therefore, in order to extract the
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A next-generation technology is nee
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Wind Dir. Figure 2. Negative ion co
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Volumetric Imaging of Materials by
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amplitude and peak frequency change
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Figure 3. 13 C NMR spectrum of corn
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Approach Two flow loops, one that o
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Modification of Ion Exchange Resins
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Permanganate Treatment for the Deco
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minimized by medium exchange. After
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Figure 1. Thermogravimetric analysi
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Validation and Scale-Up of Monosacc
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Concentration (g/100g solution) Con
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Analysis of High-Volume, Hyper-Dime
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ecent figure of merit values. Shoul
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Probabilistic Methods Development f
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a) Traditional PCA-based process co
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Acronyms and Abbreviations 2-D two-
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PNNL-13501 - Pacific Northwest National Laboratory

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